**CIGAL Reference Manual, Chapter 1 (Topics): PARADIGMS**
===== PARADIGMS -- Paradigm Overview =====
        CIGAL's REALTIME command (see \L[REALTIME][2]) can be used to execute
 experiment paradigms under real-time control.  This section describes some
 features of the current implementation of CIGAL for running functional MRI
 paradigms on the Macintosh.
     The PDIGMS menu (in the menu bar) can be used to access the standard
 paradigms currently being used at the MR Research Center at UPMC.  This
 menu also provides several general fMRI features such as for entering scan
 parameters and checking the status of the analog and digital connections.
     A paradigm actually consists of 3 parts: the paradigm program (a CIGAL
 macro program such as CHECKER.IMP), a paradigm menu file (such as
 CHECKER.MNU), and a dialog resource (such as the "checker" DLOG and DITL
 entries in the file PARADIGMS.RSRC).  Of these only the paradigm program
 is actually required, the menu file and its dialog resource are not
 required but do tend to make the paradigm easier to use.

The paradigm program:
     Most paradigms are written in a standard format.  This consists of the
  following 8 sections:
  1) Code to declare data variables (note, most should be declared as GLOBAL).
     Many standard paradigm variables are also declared by the macro
     PDIGMINIT which is run when CIGAL starts up.  These variables should be
     declared and initialized if they do not already exist or if the macro
     is called with 0 as the first argument.
  2) Code to store the values of all important variables in a parameter file.
     This is executed when the first argument is 4 or 5; variable names and
     values are written using the DUMP command (see \L[DUMP][2]).
  3) Code to create data displays if necessary.
  4) A call to the PDIGMBLOCKS macro to convert the block sequence specified
     in the menu into tables giving the code value, block time and number of
     trials for each block.  This step also checks to see if the paradigm is
     being run in PRACTICE mode, in which case the DISDAQS are ignored, or in
     TEST mode, in which case there are no DISDAQS and all block times are
     divided by 10 to run faster.
  5) Code to generate data tables to be used for the individual trials.  This
     section does most of the work of the paradigm by creating all the data
     necessary to specify the entire paradigm. Typically it includes some
     initialization steps and then a WHILE loop that makes entries appropriate
     for each individual block of trials.
  6) A call to the READYSCAN macro to do standard steps like calculating the
     number of images per slice and waiting for the MR operator to finish
     scanner setup operations (including any prescanning).  READYSCAN also
     allows you to call the NEAREAL menu to prepare for near real-time fMRI
     data analysis if that is desired.  [Note: NEAREAL is not yet available]
  7) The REALTIME command containing the code to be executed during the
     paradigm by the REALTIME processor.  This code constitutes the paradigm
     itself, which mostly just steps through the data variables created in
     step 5 above.  See \L[REALTIME][2] and \L[RT_PROCESSOR][6] for more on this.
  8) Code to save the paradigm data, if the paradigm was run using the menu's
     START option (e.g. $1 == 1; TEST and PRACTICE run the paradigm but don't
     store any data).  The data are written to a data management file using
     CIGAL's DMWRITE command (see \L[DMWRITE][2]).  The SAVEPDDATA macro expects
     the paradigm name as an argument and then puts a copy of the paradigm
     program (e.g. the CHECKER.IMP file), a list of the paradigm's parameter
     settings, the REALTIME runlog, cardiac and respiratory data if collected,
     and a copy of the STIMREC file (created for use in AVS data analysis)
     into a single DM format file.  The file name is specified using the
     scanner's study, series, and image numbers so these values must all be
     entered before the file is created.

The paradigm menu file:

The menu file is a standard CIGAL screen menu specification file. It
lists the CIGAL commands that are to be executed when different fields in
the displayed menu are activated.  See \L[MENUS][1] for more on CIGAL menus.
The DIALOG command is used to transfer values back and forth between the
variables in the menu file and the displayed menu (see \L[DIALOG][3]). See
\L[MENU][2] for how to load and control displayed menus.

The paradigm menu resources:

Typically a paradigm menu is associated with a DLOG and a DITL
resource in the file PARADIGMS.RSRC.  These resources are created using a
resource editor such as RESEDIT (which is not part of the CIGAL package).
The menu file and the menu resources should all have the same name (which
currently can be no longer than 8 characters); this is usually the same as
the name of the paradigm program.

Once a menu file and its associated resources are created they are
bound together and loaded into CIGAL's MENUS file using the MENU command
(e.g. menu pdigmname 32).

[Note: CIGAL will soon be able to create and edit resources directly,
thus facilitating making dialog menus.]


**See Also:**\\
[[jvs:cigal:manual:chapter3:dialog|DIALOG(3)]], 
[[jvs:cigal:manual:chapter2:dmwrite|DMWRITE(2)]], 
[[jvs:cigal:manual:chapter2:dump|DUMP(2)]], 
[[jvs:cigal:manual:chapter2:menu|MENU(2)]], 
[[jvs:cigal:manual:chapter1:menus|MENUS(1)]], 
[[jvs:cigal:manual:chapter2:realtime|REALTIME(2)]], 
[[jvs:cigal:manual:chapter6:rt_processor|RT_PROCESSOR(6)]]

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